Re: Bug Report: Creating a hardlink to any of the file in git repo cause the source file to show up in git commit message editor under "Changes not staged for commit" section.

Michael <git-scm@webhippo.net> writes:

This does not have to do anything with hardlink. A simple "touch" should do as long as FILE2/FILE3 are sufficiently old.

You are smudging cached stat information in your pre-commit hook (st_ctime would be different), and that is shown as a difference between the working tree and the index (note that nowhere in githooks documentation we say pre-commit hook is allowed to muck with the working tree files). I think we do refresh the cached stat information before running the pre-commit hook so that the hook can check the list of working tree files that are different from the index using diff-files, but the purpose of the said hook is to validate, and not affect, the state of the working tree, and I wouldn't be surprised if we do not update the cached stat information after the hook returns control to us.

If you really want to munge the working tree inside pre-commit, I think adding "git update-index --refresh" at the end of pre-commit hook would make the phantom change go away.